# 使用 Homebrew, apt, Nix 安装 mmseqs2 查看 mmseqs2 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。 ## 安装 ```sh sudo av install brew:mmseqs2 ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install mmseqs2 ``` 证据: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install mmseqs2 ``` 证据: Debian stable package indexes: mmseqs2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#mmseqs2 ``` 证据: nixpkgs package indexes: pkgs/by-name/mm/mmseqs2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## 软件包事实 - **软件包键:** brew:mmseqs2 - **软件包管理器:** Homebrew - **软件包管理器页面:** - **版本:** 18-8cc5c - **来源摘要:** Software suite for very fast sequence search and clustering - **主页:** - **仓库:** - **上游文档:** - **许可证:** MIT - **源码归档:** - **已生成:** 2026-08-04T22:13:35+00:00 ## 可执行文件 - mmseqs (cli) - mmseqs (别名) ## 依赖 - libomp - wget ## 构建依赖 - cmake ## macOS 提供的库 - bzip2 ## 安装行为 - post-install 钩子: 未定义 - Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## 版本和新鲜度 - 页面生成时间: 2026-08-04 - 管理器版本: 18-8cc5c - 本地数据: OK - 上游仓库: https://github.com/soedinglab/MMseqs2 - 信息: No package-manager update timestamp was available. - 信息: No cached GitHub release or tag data was available. ## 项目历史与用法 MMseqs2, short for Many-against-Many sequence searching, is a bioinformatics suite from Martin Steinegger, Johannes Soding, and collaborators for searching and clustering very large protein and nucleotide sequence sets. The project README describes it as open-source C++ software for Linux, macOS, and Windows via Cygwin, built for multicore and multi-server scalability. Its 2017 Nature Biotechnology paper introduced MMseqs2 as a sensitive protein sequence search tool for massive datasets, and the project documentation frames it as much faster than BLAST while preserving high sensitivity at practical search settings. ### 项目历史 Its major technical milestones followed the growth of public sequence databases. The 2018 Nature Communications Linclust paper integrated a linear-time clustering workflow into MMseqs2, demonstrating clustering of 1.6 billion metagenomic protein fragments in 10 hours on a single server and showing why quadratic or near-quadratic approaches such as CD-HIT and UCLUST struggled at that scale. A 2019 Bioinformatics paper expanded the ecosystem with an MMseqs2 desktop and local web-server app for interactive searches through custom protein sequence and profile databases, reducing query overhead and exposing MMseqs2 to users outside command-line-only workflows. ### 使用方式 In practice, users run the `mmseqs` executable as a suite of modules and workflows: creating MMseqs2 databases from FASTA or FASTQ, running `easy-search` for sequence search, `easy-cluster` for cascaded clustering, `easy-linclust` for larger datasets, converting alignment results, and using GPU-backed search modes where available. Its package-manager niche is scientific computing rather than general CLI tooling: Homebrew, Debian, Ubuntu, and Nix packages make a research-grade sequence analysis engine available to workstation and server users without building the full C++ stack by hand. ### 来源 - - - - - - ## 安全说明 infrastructure mutation or orchestration signal. - **Geiger 风险:** orange / 中 - infrastructure mutation or orchestration signal ## 源数据库详情 - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** mmseqs2 - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## 其他软件包管理器记录 - Debian apt - mmseqs2 - 15-6f452+ds-2+b3: normalized package name match | Debian stable package indexes: mmseqs2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | ultra fast and sensitive protein search and clustering | https://github.com/soedinglab/MMseqs2 - Debian apt - mmseqs2-examples - 15-6f452+ds-2: normalized package name match | Debian stable package indexes: mmseqs2-examples from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | optional resources for the mmseqs2 package | https://github.com/soedinglab/MMseqs2 - Nix - mmseqs2: normalized package name match | nixpkgs package indexes: pkgs/by-name/mm/mmseqs2/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - mmseqs2 - 15-6f452+ds-2: normalized package name match | Ubuntu 24.04 LTS package indexes: mmseqs2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | ultra fast and sensitive protein search and clustering | https://github.com/soedinglab/MMseqs2 - Ubuntu apt - mmseqs2-examples - 15-6f452+ds-2: normalized package name match | Ubuntu 24.04 LTS package indexes: mmseqs2-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | optional resources for the mmseqs2 package | https://github.com/soedinglab/MMseqs2 ## 相关链接 - [Secret-risk packages](https://pkg.so/zh-hans/secret-risk-packages/) - Has protected-tool coverage, approval-gate, or non-low Geiger security signals. - [Terminal utility packages](https://pkg.so/zh-hans/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Text processing packages](https://pkg.so/zh-hans/text-processing-tools/) - Matched text, document, or structured-data processing metadata. - [Networking and protocol packages](https://pkg.so/zh-hans/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [wget](https://pkg.so/zh-hans/brew/wget/) - Runtime dependency declared by Homebrew. - [cmake](https://pkg.so/zh-hans/brew/cmake/) - Build dependency declared by Homebrew. - [seqkit](https://pkg.so/zh-hans/brew/seqkit/) - Shares pkgdb curated category or tags: bioinformatics, cli, science, sequence-analysis. - [seqtk](https://pkg.so/zh-hans/brew/seqtk/) - Shares pkgdb curated category or tags: bioinformatics, cli, science, sequence-analysis. - [kraken2](https://pkg.so/zh-hans/brew/kraken2/) - Shares pkgdb curated category or tags: bioinformatics, cli, metagenomics, science. - [paml](https://pkg.so/zh-hans/brew/paml/) - Shares pkgdb curated category or tags: bioinformatics, cli, protein-sequences, science. - [ropebwt3](https://pkg.so/zh-hans/brew/ropebwt3/) - Shares pkgdb curated category or tags: bioinformatics, cli, science, sequence-search. - [skani](https://pkg.so/zh-hans/brew/skani/) - Shares pkgdb curated category or tags: bioinformatics, cli, metagenomics, science. - [bracken](https://pkg.so/zh-hans/brew/bracken/) - Shares pkgdb curated category or tags: bioinformatics, cli, metagenomics, science. - [samtools](https://pkg.so/zh-hans/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [kalign](https://pkg.so/zh-hans/brew/kalign/) - Local package facts share a topical domain. Shared terms: analysis, bioinformatics, cli, fast, libomp. ## Combined YAML source View the package source record on GitHub. [combined/mmseqs2.yml](https://github.com/mxcl/pkgdb/blob/main/combined/mmseqs2.yml) ## 来源 - pkg.so package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - pkgdb category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph